Pinned Repositories
copykat_pipeline
icgc_consensus_copynumber
ICGC PCAWG-11 consensus copy number pipeline
icgc_consensus_purity
icgc_copynumber_event_inventory
Code to create a copynumber event inventory for ICGC PCAWG
icgcConsensusCN_to_BB
Parser for ICGC consensus CN to Battenberg format
qdnaseq_pipeline
randomclone
Establish random subclonal reconstructions from mutation data
targeted_het_snp_imbalance
Pipeline to call significant imbalance of heterozygous SNPs
sdentro's Repositories
sdentro/copykat_pipeline
sdentro/icgc_consensus_copynumber
ICGC PCAWG-11 consensus copy number pipeline
sdentro/icgc_consensus_purity
sdentro/randomclone
Establish random subclonal reconstructions from mutation data
sdentro/icgc_copynumber_event_inventory
Code to create a copynumber event inventory for ICGC PCAWG
sdentro/icgcConsensusCN_to_BB
Parser for ICGC consensus CN to Battenberg format
sdentro/qdnaseq_pipeline
sdentro/targeted_het_snp_imbalance
Pipeline to call significant imbalance of heterozygous SNPs
sdentro/battenberg
Battenberg R package for subclonal copynumber estimation
sdentro/Battenberg_chrY_SNPs
Script to create Y chromosome SNPs for Battenberg
sdentro/battenberg_logr_totalcn
Estimate total copy number from logR data
sdentro/battenberg_templates
Battenberg output templates
sdentro/clonality_management
sdentro/copynumber
Bioconductor copynumber package with hg38 and mm10
sdentro/dockstore-cgpwgs
Dockstore implementation of CGP core WGS analysis
sdentro/dpclust
Dirichlet Process based methods for subclonal reconstruction of tumours
sdentro/dpclust3p
Dirichlet Process Clustering Pre-Processing Pipeline
sdentro/generate_icgc_batch_overview
sdentro/icgc_consensus_clustering_assignment
ICGC PCAWG-11 pipeline used for assignment of SNVs, Indels and SVs to consensus mutation clusters
sdentro/icgc_resolve_wgd
sdentro/icgc_summary_table
sdentro/modern-unix
A collection of modern/faster/saner alternatives to common unix commands.
sdentro/MutationTime.R
An R script to time somatic mutations
sdentro/nextflow_allelecounter
Nextflow implementation of the alleleCounter tool
sdentro/QDNAseq
QDNAseq package for Bioconductor
sdentro/randomclone_smchet_docker
RandomClone Single SMC-het pipeline
sdentro/replication_summarise
Code to summarise replication timing data
sdentro/scCNA
R package for logR-based copy number profiling for shallow coverage/single cell (SC) experiments
sdentro/smchet_utils
Functions for SMC-het pipelines
sdentro/TidyTuesday
📊 My contributions to the #TidyTuesday challenge